# Package picard.util

package picard.util

Related Packages
Package
Description
picard
picard.util.help
picard.util.IntervalList
Class
Description
AbstractInputParser
Class for parsing text files where each line consists of fields separated by whitespace.
AccumulateQualityYieldMetrics
Combines multiple Picard QualityYieldMetrics files into a single file.
AdapterMarker
Store one or more AdapterPairs to use to mark adapter sequence of SAMRecords.
AdapterPair
AlleleSubsettingUtils
Utilities class containing methods for restricting `VariantContext` and `GenotypesContext` objects to a reduced set of alleles, as well as for choosing the best set of alleles to keep and for cleaning up annotations and genotypes after subsetting.
AsyncIterator<T>
Wrapper around a CloseableIterator that reads in a separate thread, for cases in which that might be efficient.
AtomicIterator<T>
Describes
BaitDesigner
Designs baits for hybrid selection!
BaitDesigner.DesignStrategy
Set of possible design strategies for bait design.
BarcodeEditDistanceQuery
A class for finding the distance between multiple (matched) barcodes and multiple barcode reads.
BasicInputParser
TextFileParser which reads a single text file.
BedToIntervalList
CircularByteBuffer
Implementation of a circular byte buffer that uses a large byte[] internally and supports basic read/write operations from/to other byte[]s passed as arguments.
ClippingUtility
Utilities to clip the adapter sequence from a SAMRecord read
CsvInputParser
DbSnpBitSetUtil
Utility class to use with DbSnp files to determine is a locus is a dbSnp site.
DbSnpBitSetUtil.DbSnpBitSets
Little tuple class to contain one bitset for SNPs and another for Indels.
DelimitedTextFileWithHeaderIterator
Iterate through a delimited text file in which columns are found by looking at a header line rather than by position.
FifoBuffer
Summary
GraphUtils
Created by farjoun on 11/2/16.
GraphUtils.Graph<Node extends Comparable<Node>>
IlluminaUtil
Misc utilities for working with Illumina specific files and data
IlluminaUtil.IlluminaAdapterPair
Describes adapters used on each pair of strands
IntervalListToBed
Trivially simple command line program to convert an IntervalList file to a BED file.
IntervalListTools
Performs various `IntervalList` manipulations.
IntervalListTools.Action
Iterators
LiftOverIntervalList
This tool adjusts the coordinates in an interval list on one reference to its homologous interval list on another reference, based on a chain file that describes the correspondence between the two references.
LiftoverUtils
MathUtil
General math utilities
MathUtil.LogMath
A collection of common math operations that work with log values.
PropertyUtils
Utility for loading properties files from resources.
QuerySortedReadPairIteratorUtil
A collection of helper utilities for iterating through reads that are in query-name sorted read order as pairs
QuerySortedReadPairIteratorUtil.ReadPair
ReflectionUtil
Class which contains utility functions that use reflection.
RExecutor
Util class for executing R scripts.
ScatterIntervalsByNs
A Tool for breaking up a reference into intervals of alternating regions of N and ACGT bases.
ScatterIntervalsByNs.ScatterIntervalsByNReferenceArgumentCollection
SequenceDictionaryUtils
Class with helper methods for generating and writing SequenceDictionary objects.
SequenceDictionaryUtils.SamSequenceRecordsIterator
SingleBarcodeDistanceMetric
A class for finding the distance between a single barcode and a barcode-read (with base qualities)
TabbedInputParser
Parser for tab-delimited files
TabbedTextFileWithHeaderParser
Parse a tabbed text file in which columns are found by looking at a header line rather than by position.
ThreadPoolExecutorUtil
ThreadPoolExecutorWithExceptions
This version of the thread pool executor will throw an exception if any of the internal jobs have throw exceptions while executing
UnsignedTypeUtil
A utility class for dealing with unsigned types.
VariantType
Enum to hold the possible types of dbSnps.